Inport data
results <- read.csv("results.csv") %>%
mutate(RR=exp(Value),
"95%CI" =paste0(format(round( exp(Value -1.96*Std.Error), digits = 3),nsmall=3)," - " ,
format(round(exp( Value +1.96*Std.Error), digits = 3),nsmall=3))) %>%
mutate(SA3_CODE16=as.character(SA3_CODE16)) %>%
mutate(RR=round(RR,2),
IRSAD=round(IRSAD,0)) %>%
mutate(Population=factor(Population,levels=c("Age 12-17", "Age 18-25", "Females", "Males", "All young people"))) %>%
mutate(Sum= paste0(format(RR, nsmall=2), " 95% CI:",`95%CI`)) %>%
mutate(RR=ifelse(IRSAD <=810,NA,RR),
Sum=ifelse(IRSAD <=810,NA,Sum))
dta <- readRDS( here("COVID","COVID_cleaned.rds"))
map <- readRDS(here("Data", "Shapefile_SA3.rds"))
map@data <- map@data %>%
left_join(results %>% filter( Population == "All young people" ) , by = "SA3_CODE16")
map <- sf::st_as_sf(map)
Plot
dta<-results %>%
#3 sa3 excluded at the tail
dplyr::filter( IRSAD > 810)
dta <- highlight_key(dta, ~SA3_NAME)
plot<- ggplot(dta, aes(x=IRSAD, y=RR,fill="")) +
geom_point( aes(text=paste0(SA3_NAME,"\nRR: ",format(RR, nsmall=2),
" 95% CI:",`95%CI`),fill="#0072B2"),
alpha=0.6, col="#0072B2", size=1)+
geom_smooth(col="red",span=1,se=FALSE) +
facet_wrap( ~ Population,ncol = 5)+
theme_bw() +
theme(legend.position = "none",
strip.background=element_rect(fill="white"))
## Warning: Ignoring unknown aesthetics: text
bs_gg2 <- ggplotly(plot,tooltip="text",
height = 400,
width = 800)
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
highlight(bs_gg2)
## Setting the `off` event (i.e., 'plotly_doubleclick') to match the `on` event (i.e., 'plotly_click'). You can change this default via the `highlight()` function.
Map
bins <- c(0.6,0.7, 0.8, 0.9,1.0 ,1.1, 1.2, 1.3,1.4, Inf)
pal <- leaflet::colorBin("YlGnBu", domain = map$RR, bins = bins)
labels <- sprintf(
"<strong>%s</strong><br/> RR: %s",
map$SA3_NAME16, map$Sum
) %>% lapply(htmltools::HTML)
sd <- highlight_key(map, ~SA3_NAME16 )
map1<- leaflet(sd) %>%
addPolygons(color = "#444444",
weight = 1,
smoothFactor = 0.5,
opacity = 1.0, fillOpacity = 0.5,
fillColor = ~pal(RR),
label = labels,
highlightOptions = highlightOptions(
color = "white", weight = 2,
bringToFront = TRUE))
## Warning: sf layer has inconsistent datum (+proj=longlat +ellps=GRS80 +no_defs).
## Need '+proj=longlat +datum=WGS84'
plot<- ggplotly(ggplot(sd, aes(x=IRSAD, y=RR)) +
geom_point( aes(text=paste0(SA3_NAME,"\nRR",format(RR, nsmall=2),
" 95% CI:",`95%CI`)),
alpha=0.6, col="#0072B2", size=1)+
geom_smooth(col="red",span=1,se=FALSE) +
xlim(840,1180)+
theme_bw() +
theme( strip.background=element_rect(fill="white")),
height = 400, width = 400)
## Warning: Ignoring unknown aesthetics: text
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## Warning: Removed 8 rows containing non-finite values (stat_smooth).
withr::with_options(
list(persistent = TRUE),
crosstalk::bscols(widths = c(6, 6),map1, plot)
)